In fact, we can consider Bioremediation 3. There are at least three aspects in which such an encounter may bring about entirely new angles to the subject. The primary feature is the current ease of analyzing and genetically programming many types of microorganisms of environmental relevance such as Pseudomonads Nikel et al. This facilitates and accelerates studies on bottlenecks that limit catabolism of the compounds of interest, whether enzymatic, regulatory, or physiological.
In some cases, it has been possible to create new enzymes from scratch through a combination of rational protein design and directed evolution approaches Kan et al. This opens amazing opportunities to engineer agents able to cope with new types of chemicals for which nature has not yet invented a biodegradative solution. Efforts to develop new whole-cell catalysts are also assisted by computational platforms that guide the assembly of new pathways by automatically searching in databases the best enzyme and genes to deliver the activities of interest. The resulting pathways involve known and novel enzymatic steps that may indicate unidentified enzymatic activities as well as providing potential targets for protein engineering to alter substrate specificity.
Thereby assembled pre-pathways could then be optimized by playing in vivo with the wealth of biological parts available through various repositories of promoters and other regulatory components e. The objective of such an optimization is not so much to express the desired catalytic activity at very high levels, as to ensure that the genetic implants nest well within the broader regulatory and enzymatic network of the host. As mentioned above, the retroactivity between the genetic constructs and the genomic and biochemical chassis of the carrying bacteria Fig.
But the question remains on how to deliver biodegradative activities to a target site and how to scale this up to tackle global pollutants. The single-cell catalyst versus the catalytic consortium dilemma. However, the background metabolic network of such a single-compartment reactor may not be optimal for each biochemical step of the route. Finally, the tridimensional structure of microbial consortia makes a difference in the efficiency of the processes that they catalyze.
Designing the architecture of a multi-strain agent thus becomes another point of action where systems-guided engineering can be applied for the sake of better remediating activities. A side-benefit of utilizing communities rather than single strains is that one can artificially assemble a catalyst by putting together specimens that naturally bear one or more of the steps of a pathway of interest.
In this case, when brought together, the consortium displays the desired metabolic capacity Zhou et al. Doing this requires a deep knowledge of the metabolic networks of each of the components of the group, but it has the advantage of resulting in a biological material that is not genetically modified. The new wave of Biodegradation could thus expand the former focus on assembling pathways and constructing degradative superbugs towards engineering catalysts in their entirety, including consortia with a desirable physical shape. This takes us to the final feature of systemic bioremediation: rational spreading of biodegradative activities.
As mentioned above, quite in contrast with the many pathway assembly methods there are only a few advanced technologies for releasing catabolic agents to the environment — whether natural or GM — in an efficacious form beyond mere spreading of the agents in a aqueous suspension. These include inter alia formulations with plant seeds e. In many instances, such carriers are combined with additives that prolong the lifespan and shelf life of the biological components. Larger-scale bioremediation interventions may combine also biological activities with some type of civil engineering e.
DNA propagates very quickly through the multiscale complexity pyramid.
As the studies on global spread of antibiotic resistance have shown, mutations that emerge in a single genome may spread very rapidly through a suite of horizontal gene transfer mechanisms to eventually reach out virtually every ecosystem — provided that there is a strong selective pressure to do so. We argue that Bioremediation research could learn from such mechanisms of dispersal in order to engineer dissemination of beneficial traits e.
In sum: while the science of biodegradation will remain focused on pathways, hosts, communities, and their interplay with the physicochemical constituencies of polluted site, the technology of bioremediation will move forward taking stock of past failures and capitalizing on the many opportunities and tools brought up by contemporary systems and synthetic biology. This includes methods that allow assembly of new pathways and enhancement of the catabolic capacity of a large community without necessarily relying on the release of transgenic GMOs.
Although the primary reason for the difficulties of Bioremediation 2. While massive evidence indicates that the impact of recombinant microorganisms when released for bioremediation purposes is not worse than naturally occurring counterparts, a large part of the public still invokes the Black Swan 1 argument Taleb to oppose any purposeful liberation of genetically manipulated agents. The first concern is about the spreading non-natural genetic information e. Early in the history of Bioremediation 2. This was due to spontaneous mutations and the activity of mobile insertion sequences, an issue hardly tractable by that time.
This same question has been picked again more recently by synthetic biologists in the pursuit of certainty of containment CoC for highly refactored microorganisms. The favourite approach in this case involves the emancipation of one of the stop codons and its recoding to guide insertion of non-natural amino acids in the structure of essential proteins. This makes viability of the bacterium entirely dependent on addition to the medium of such chemically synthesized amino acid Rovner et al.
Although the level of containment of such strains is extraordinary compared to previous ones, they are still above CoC. Attempts to move the figure still further up involve altering the genetic code, bear the genetic information in a non-DNA molecule, or replace one or more of the nucleotides with chemically synthesized alternatives Schmidt and de Lorenzo , In this way, the thereby modified genetic information could not be read by any potential capturer, which could not interpret standard DNA either. Whether or not these approaches will be useful for agents to be released is unclear, because the resulting strains may have lost much of the necessary competitive fitness of naturally occurring bacteria.
And in any case, it is unlikely that the anti-GMO community could accept strains that are far more engineered than the first generation of environmental recombinants.
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Is there a way of producing advanced and efficacious bioremediating agents or strategies that circumvent this problem and thus ease public sympathy for the technology? In the paragraphs above, we have hinted at some approaches to this challenge. This opens a window of opportunity for their application to problems that were not amenable before because of the transgenic tag. A second possibility is systems-guided assembly of naturally occurring strains to form a catalytic consortium, with the added advantages mentioned before readjusting of expression levels and possibilities to design their 3D architecture.
However, the question remains on whether we can develop new catabolic and enzymatic activities without resorting to genetic engineering. To address how biodegradation and bioremediation research may look like in the future, it is useful to look back into some of the earlier studies, in particular what was called by the time plasmid-assisted molecular breeding Kellogg et al. The key idea was to start with a complex community of microorganisms retrieved from sites with a history of pollution by the target compound, some of which bearing plasmids with catabolic genes. Progressive selection of best growers in a chemostat eventually led to isolation of strains that incorporated in their genome the complement of genes that could afford biodegradation of an otherwise recalcitrant compound e.
The solution to the metabolic problems was thus the result of horizontal gene transfer and spontaneous mutagenesis. Although the method was well-liked for a while, it was soon replaced by more directed approaches where the user had a better control of the changes leading to a degradative phenotype.
The positive side of molecular breeding was, however, that the resulting strains were not GMOs and the assembled pathways non-recombinant, thereby enabling their immediate application if necessary. And the result is a physical entity a strain that has gone through a multi-objective optimization.
We argue that such methodology could be revisited in the times of systemic biology for generating new strains and properties that may not be amenable to forward design with the level of knowledge we have today. The stress-genetic innovation cycle. The figure sketches how metabolic troubles e. Bio-based approaches to tackle environmental pollution, from prevention to global-scale remediation. The direction of the arrow indicates the increasing complexity and diversification of the technologies involved see de Lorenzo et al.
Some of the items shown in the flow are addressed separately in other Volumes of this series. Most contributions that follow this Introductory Chapter to the volume on biodegradation and bioremediation bear witness of the impasse triggered by the transition between stages 2. The former emphasis on genetic engineering as the main driver of the field has been largely left aside in favor of less risky and more acceptable approaches based on sound microbial ecology, geobiochemistry, and physicochemical methods.
Also, the articles reflect the effort to understand in detail what is going in the biological realm during natural attenuation of pollution with or without much human intervention e. But also, a large share of the work herein reported capitalizes on the suite of omics technologies that allow a detailed follow up of responses of individual strains, community composition, and activity monitoring in very different bioremediation scenarios. In the meantime, new and acute environmental challenges have become noticeable and cannot be ignored e.
A new encounter between the immense possibilities of these new fields and the pursuit of remedies for both chronic and new environmental problems is not only desirable but also unavoidable. And some of the chapters also testify that frontline technologies can open avenues for solving thus far intractable pollution puzzles. The metaphor developed by Nassim Taleb to argue that the non-occurrence of a certain event thus far is not an evidence that it cannot happen. Skip to main content Skip to sections. Advertisement Hide. Biodegradation and Bioremediation: An Introduction.
Living reference work entry First Online: 18 June Download reference work entry PDF. Intuitively one envisages pollutants as a suite of chemicals of either natural or synthetic origin which, once released into the environment, causes the malfunction of one or more components of an otherwise balanced niche or ecosystem. There are compounds that are completely natural e. Others are entirely human-made xenobiotics e. They might be released to the environment deliberately e. Their detrimental effects can stem from the inherent properties of the product or may reside in the harmful qualities of their synthesis intermediates or their partial metabolism.
Finally, their chemical structures might be amenable to total or limited microbial transformations under specific circumstances — or recalcitrant to biodegradation and thus persist in the afflicted sites for long periods of time. The functionalities of these molecules are very diverse Fig. We leave deliberately heavy metals and metalloids aside the picture, as they raise a different type of problems and possible solutions.
Also, whereas intuitively one tends to picture pollutants as structurally intricate toxic compounds e. By the same token, some bioactive molecules e.
Biodegradation and Bioremediation: An Introduction | SpringerLink
The status of specific chemical species as environmental pollutants goes much beyond their inherent toxicity to biological systems, but encompasses at least the six parameters pictured in Fig. Open image in new window. There are various follow-up developments that stem from such state of affairs. First , the biodegradation and bioremediation research of the s—s suggested that one has to consider the target sites as a whole system, including the physicochemical and geological characteristics of the place, the ecology and dynamics of the native microbial community, and the catalytic potential of biological and non-biological components — including what could be called the post-mortem enzymatic activities of many microorganisms French et al.
While the complexity of such systems is indeed high, they offer entirely new opportunities to address them with the tools of systems biology and systems science — which were not available before. Second , GM strains with enhanced or entirely new catabolic activities that do well under controlled laboratory conditions generally perform poorly when released into the environment. This is connected to the long-standing biotechnological challenge of how to genetically program microorganisms to stably behave as desired.
The issue of retroactivity Gyorgy and Del Vecchio and metabolic burden Ceroni et al. What one could call Environmental Galenic Science i. The wealth of information on the genetic and biochemical diversity of the microbiota that thrives in polluted sites has enabled the setup of bio-based alternatives to chemical processes with whole-cell biocatalysts developed through metabolic engineering. Conspicuous examples include degradable polymers, biofuels and both bulk and fine chemicals, which are bound to take over a large portion of the current market, as oil becomes more and more scarce and expensive as the feedstock for their production Chae et al.
Furthermore, many emissions can be biologically met at the point of manufacturing, thereby preventing their eventual release and live catalysts can be integrated in zero-pollution industrial pipelines. Indirectly, the onset of biological manufacturing of more and more added-value chemicals contribute to sustainability by replacing otherwise polluting chemical processes. But the direct environmental dividends of the efforts done for two decades on molecular biodegradation and in situ bioremediation research have hardly materialized and the most popular technologies for in situ cleanup to this day largely involve attenuation and bio-stimulation e.
A second characteristic of Bioremediation 3. Having one sole strain as the recipient of a complete pathway makes regulation of expression of the genes of interest the only possibility for adjusting the right dose of activity required for a specific application. In reality, it is unusual to find naturally occurring strains that can run by themselves a complex route, in particular for very novel compounds. A consortium can not only divide the catabolic labor between its various components but also let new functions to emerge that could not happen in single cells Fig.
For instance, one member of the community may not contribute to catabolism of the target molecule, but might eliminate an intermediate toxic side-product. Moreover, the tuning of the optimal doses of biochemical activities for each step of the degradative route can be adjusted not just by endogenous, e. Since the enzymes and transcription factors involved in many biodegradative pathways are often promiscuous, the catabolic capacity of a consortium is often higher than the sum of their components, a phenomenon known as ectopic metabolism de Lorenzo et al.
In the meantime, data on massive horizontal gene transfer has revealed how quickly a new trait e. Under the right conditions, DNA seems to move easily through the entire complexity pyramid Fig. The idea of developing DNA super-donors able to implant and propagate particular activities in a community of recipients has been considered at various times throughout the history of bioremediation Top et al. Alas, the genetic tools available to engineer such occurrences were very limited and the concept has not been really developed to its full potential.
But, this is not the end of the notion. There is a suite of plasmid-based DNA transfer systems that are promiscuous and active enough to think along the line. Furthermore, the role of phages to propagate new genotypes in a large bacterial population is becoming increasingly evident von Wintersdorff et al. However, expression signals vary dramatically from one host to the other, and one pathway engineered in E. The problem remains, however, on how to foster propagation of preset DNA sequences in the absence of a major selective pressure.
In reality, this challenge is by no means exclusive of large-scale bioremediation, but it is a general one: how to stimulate propagation of beneficial traits through a population without an exogenous force to push it. For diploid species, a sophisticated strategy called gene drives has been developed which allows transmission of a given genetic cargo to the progeny at frequencies above the mere Mendelian distribution of inherited traits Champer et al. After a few reproductive cycles, this allows them to eventually spread to all members of the target population. The potential power of the technology has raised serious safety concerns, as the method could be use to precisely eliminate particular species e.
But by the same token, one could think on using the approach for dissemination of activities that are intrinsically beneficial for the environment, e. That bacteria are generally haploids prevents doing something similar to what has been successfully attempted in yeasts and animals, but one could entertain scenarios in which cargoes engineered inside promiscuous plasmids or phages are directed to very conserved chromosomal regions of a suite of species and force recombination or else die.
Whether adopting this strategy or formulating others for spreading DNA-bearing biodegradative activities rather than degradative strains remain one of the key challenges in the field. In this respect, while Bioremediation 2. The much-debated geoengineering of planet Earth could potentially be complemented or even replaced by large-scale bioremediation strategies to capture CO 2 and to improve the capacity of marine microorganisms to act on plastics and other globally widespread micropollutants.
The term co-metabolism is often used to indicate the non-beneficial to the microorganism biochemical pathways concerned with the biodegradation of xenobiotics. However, co- metabolism depends on the presence of a suitable substrate for the microorganism. Such compounds are referred to co-substrates. Several factors influence biodegradation. These include the chemical nature of the xenobiotic, the capability of the individual microorganism, nutrient and O 2 supply, temperature, pH and redox potential. Among these, the chemical nature of the substrate that has to be degraded is very important.
Presence of cyclic ring structures and length chains or branches decrease the efficiency of biodegradation. Molecular orientation of aromatic compounds influences biodegradation i. Besides the factors listed above, there are two recent developments to enhance the biodegradation by microorganisms. This is a process by which the microbial activity can be enhanced by increased supply of nutrients or by addition of certain stimulating agents electron acceptors, surfactants.
It is possible to increase biodegradation through manipulation of genes. More details on this genetic manipulation i. Several enzyme systems with independent enzymes that work together are in existence in the microorganisms for the degradation of xenobiotics. The genes coding for the enzymes of bio-degradative pathways may be present in the chromosomal DNA or more frequently on the plasmids. In certain microorganisms, the genes of both chromosome and plasmid contribute for the enzymes of biodegradation.
The microorganism Pseudomonas occupies a special place in biodegradation. A selected list of xenobiotics and the plasmids containing the genes for their degradation is given in Table There are certain compounds that do not easily undergo biodegradation and therefore persist in the environment for a long period sometimes in years. They are labeled as recalcitrant. There may be several reasons for the resistance of xenobiotics to microbial degradation:. The compounds may be highly toxic or result in the formation highly toxic products that kill microorganisms.
There are a large number of racalcitrant xenobiotic compounds e. A group of microorganisms Aspergillus flavus, Mucor aternans, Fusarium oxysporum and Trichoderma viride are associated with the slow biodegradation of DDT. The phenomenon of progressive increase in the concentration of a xenobiotic compound, as the substance is passed through the food chain is referred to as bio-magnification or bioaccumulation. For instance, the insecticide DDT is absorbed repeatedly by plants and microorganism.
When they are eaten by fish and birds, this pesticide being recalcitrant, accumulates, and enters the food chain. Thus, DDT may find its entry into various animals, including man. DDT affects the nervous systems, and it has been banned in some countries.
Biodegradation and Bioremediation
The most important aspect of environmental biotechnology is the effective management of hazardous and toxic pollutants xenobiotics by bioremediation. The environmental clean-up process through bioremediation can be achieved in two ways—in situ and ex situ bioremediation. In situ bioremediation involves a direct approach for the microbial degradation of xenobiotics at the sites of pollution soil, ground water. Addition of adequate quantities of nutrients at the sites promotes microbial growth. When these microorganisms are exposed to xenobiotics pollutants , they develop metabolic ability to degrade them.
The growth of the microorganisms and their ability to bring out biodegradation are dependent on the supply of essential nutrients nitrogen, phosphorus etc. In situ bioremediation has been successfully applied for clean-up of oil spillages, beaches etc. There are two types of in situ bioremediation-intrinsic and engineered. The inherent metabolic ability of the microorganisms to degrade certain pollutants is the intrinsic bioremediation. In fact, the microorganisms can be tested in the laboratory for their natural capability of biodegradation and appropriately utilized.
The inherent ability of the microorganisms for bioremediation is generally slow and limited. However, by using suitable physicochemical means good nutrient and O 2 supply, addition of electron acceptors, optimal temperature , the bioremediation process can be engineered for more efficient degradation of pollutants. The waste or toxic materials can be collected from the polluted sites and the bioremediation with the requisite microorganisms frequently a consortium of organisms can be carried out at designed places.
This process is certainly an improvement over in situ bioremediation, and has been successfully used at some places. Although it is the intention of the biotechnologist to degrade the xenobiotics by microorganisms to the advantage of environment and ecosystem, it is not always possible. This is evident from the different types of metabolic effects as shown below. Biodegradation involving detoxification is highly advantageous to the environment and population.
Certain xenobiotics which are not toxic or less toxic may be converted to toxic or more toxic products. This is dangerous. The process of conjugation may involve the conversion of xenobiotics to more complex compounds. This is however, not very common. Microbial degradation of organic compounds primarily involves aerobic, anaerobic and sequential degradation.
Aerobic biodegradation involves the utilization of O 2 for the oxidation of organic compounds. These compounds may serve as substrates for the supply of carbon and energy to the microorganisms. Two types of enzymes namely mono-oxygenases and- di-oxygenases are involved in aerobic biodegradation. Mono-oxygenases can act on both aliphatic and aromatic compounds while di-oxygenases oxidize aliphatic compounds.
Anaerobic biodegradation does not require O 2 supply. The growth of anaerobic microorganisms mostly found in solids and sediments , and consequently the degradation processes are slow. However, anaerobic biodegradation is cost- effective, since the need for continuous O 2 supply is not there. Some of the important anaerobic reactions and examples of organic compounds degraded are listed below. The term de-chlorination is frequently used for dehaiogenation of chlorinated compounds.
In the degradation of several xenobiotics, both aerobic and anaerobic processes are involved. This is often an effective way of reducing the toxicity of a pollutant. For instance, tetra chloromethane and tetrachloroethane undergo sequential degradation. Hydrocarbon are mainly the pollutants from oil refineries and oil spills. These pollutants can be degraded by a consortium or cocktail of microorganisms e. Pseudomonas, Corynebacterium, Arthrobacter, Mycobacterium and Nocardia.
The uptake of aliphatic hydrocarbons is a slow process due to their low solubility in aqueous medium. Both aerobic and anaerobic processes are operative for the degradation of aliphatic hydrocarbons. For instance, unsaturated hydrocarbons are degraded in both anaerobic and aerobic environments, while saturated ones are degraded by aerobic process. Some aliphatic hydrocarbons which are reclacitrant to aerobic process are effectively degraded in anaerobic environment e. Microbial degradation of aromatic hydrocarbons occurs through aerobic and anaerobic processes.
The most important microorganism that participates in these processes is Pseudomonas. The biodegradation of aromatic compounds basically involves the following sequence of reactions:. Most of the non-halogenated aromatic compounds undergo a series of reactions to produce catechol or protocatechuate. The bioremediation of toluene, L-mandelate, benzoate, benzene, phenol, anthracene, naphthalene, phenanthrene and salicylate to produce catechol is shown in Fig.
Likewise, Fig. Catechol and protocatechuate can undergo oxidative cleavage pathways. In ortho-cleavage pathway, catechol and protocatechuate form acetyl CoA Fig. The degraded products of catechol and protocatechuate are readily metabolised by almost all the organisms. Pesticides and herbicides are regularly used to contain various plant diseases and improve the crop yield.
In fact, they are a part of the modern agriculture, and have significantly contributed to green revolution. The common herbicides and pesticides are propanil anilide , propham carbamate , atrazine triazine , picloram pyridine , dichlorodiphenyl trichloroethane DDT monochloroacetate MCA , monochloropropionate MCPA and glyphosate organophosphate.
Most of the pesticides and herbicides are toxic and are recalcitrant resistant to biodegradation. Some of them are surfactants active on the surface and retained on the surface of leaves. Most commonly used herbicides and pesticides are aromatic halogenated predominantly chlorinated compounds. The rate of degradation of halogenated compounds is inversely related to the number of halogen atoms that are originally present on the target molecule i.
Dehalogenation i. Dehalogenation is frequently catalysed by the enzyme di-oxygenase. In this reaction, there is a replacement of halogen on benzene with a hydroxyl group. Most of the halogenated compounds are also converted to catechol and protocatechuate which can be metabolised Fig. Besides Pseudomonas, other microorganisms such as Azotobacter, Bacilluefs and E. The aromatic chlorinated compounds possessing biphenyl ring substituted with chlorine are the PCBs e.
PCBs are commercially synthesized, as they are useful for various purposes — as pesticides, in electrical conductivity in transformers , in paints and adhesives. They are inert, very stable and resistant to corrosion. However, PCBs have been implicated in cancer, damage to various organs and impaired reproductive function.
Their commercial use has been restricted in recent years, and are now used mostly in electrical transformers. PCBs accumulate in soil sediments due to hydrophobic nature and high bioaccumulation potential.
Although they are resistant to biodegradation, some methods have been recently developed for anaerobic and aerobic oxidation by employing a consortium of microorganisms. Pseudomonas, Alkali genes, Corynebacterium and Acinetobacter. For more efficient degradation of PCBs, the microorganisms are grown on biphenyls, so that the enzymes of biodegradation of PCBs are induced.
Some of the toxic organo-nitro compounds can be degraded by microorganisms for their detoxification. They contain some surfactants surface active agents which are not readily biodegradable. Certain bacterial plasmid can degrade surfactants. No single microorganism can degrade all the xenobiotics present in the environmental pollution. Certain xenobiotics get adsorbed on to the particulate matter of soil and become unavailable for microbial degradation.
It is never possible to address all the above limitations and carry out an ideal process of bioremediation. Some of these aspects are briefly described. The majority of the genes responsible for the synthesis of bio-degradative enzymes are located on the plasmids. It is therefore logical to think of genetic manipulations of plasmids. New strains of bacteria can be created by transfer of plasmids by conjugation carrying genes for different degradative pathways. If the two plasmids contain homologous regions of DNA, recombination occurs between them, resulting in the formation of a larger fused plasmid with the combined functions of both plasmids.
In case of plasmids which do not possess homologous regions of DNA, they can coexist in the bacterium to which plasmid transfer was done.